Repairing permissions is still coming up with errors in the log?? I thought after doing this, would give me a clean OS?? I'm so confused.
I've been through periods when I've had permissions that wouldn't seem to get fixed, but its not a problem unless something is actually causing you a problem.
I hope you didn't do an archive and install just because you couldn't get permission repair to come back empty! If everything is working fine, then you HAVE a 'clean OS.'